Shape key deforms edit mode / object mode after editing basis
Once Basis is deleted or edited, you will have to append an earlier saved version of the model and Join as Shapes.

Hopefully, you are doing incremental saves?

The only other option I can think of is to manually match the vertex positions, but using the 3d cursor for precision:


Select the body object > Edit Mode
Select the vertex Shift+S > Cursor to Selected, tab to Object mode
Select the head object > Edit Mode
Select the matching vertex Shift+S > Selection to Cursor
Repeat